←Back to structures

NC_025463.1__YP_009103731.1__S144_35__00035

Bact-Vir

NC_025463.1__YP_009103731.1__S144_35__00035

Identity

Accession:
NC_025463 ↗
Kingdom:
phage

Quality

78.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Shewanella_sp._phage_1/44

TaxID: 1458862

Cluster

View cluster (4 members)

3D Structure

Download PDB Download Scores JSON

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 8-49
PDB
Domain cluster: representative
CATH (18)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2lsmA00 3.40.5.70 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › DNA packaging chaperone protein FI, C-terminal beta-strand domain 0.81 71.0 6.31e-01 100.0% 78.7%
5of3A00 3.90.920.10 Alpha Beta › Alpha-Beta Complex › DNA primase, PRIM domain › DNA primase, PRIM domain 0.79 71.0 4.15e-01 100.0% 13.5%
2e9xB01 3.40.5.50 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › 0.76 69.0 5.86e-01 100.0% 68.2%
2hjqA01 3.40.5.20 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › YqbF domain 0.75 62.0 6.06e-01 100.0% 89.1%
2e9xD02 3.40.5.60 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › 0.73 60.0 5.49e-01 100.0% 85.0%
1u3oA01 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.63 52.0 4.66e-01 97.6% 93.5%
5f29B00 3.30.70.1450 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Regulator of K+ conductance, C-terminal domain 0.62 49.0 4.36e-01 100.0% 95.8%
2gs5A01 3.40.1740.10 Alpha Beta › 3-Layer(aba) Sandwich › VC0467-like › VC0467-like 0.59 48.0 3.19e-01 100.0% 21.8%
1z47A02 2.40.50.300 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.57 40.0 3.92e-01 73.8% 86.7%
1y7xA02 2.30.30.550 Mainly Beta › Roll › SH3 type barrels. › Major Vault Protein repeat 0.55 41.0 3.88e-01 100.0% 67.9%
2atzA00 3.90.920.20 Alpha Beta › Alpha-Beta Complex › DNA primase, PRIM domain › HP0184-like 0.54 44.0 3.06e-01 100.0% 40.9%
6jptA00 3.30.230.90 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.54 41.0 3.09e-01 88.1% 79.3%
1zoqA00 2.60.200.10 Mainly Beta › Sandwich › Tumour Suppressor Smad4 › 0.54 38.0 2.59e-01 78.6% 35.1%
2f2hA03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.54 41.0 4.04e-01 95.2% 81.2%
1hqmD05 3.90.105.10 Alpha Beta › Alpha-Beta Complex › Molybdopterin biosynthesis moea protein, domain 2 › Molybdopterin biosynthesis moea protein, domain 2 0.52 39.0 3.52e-01 100.0% 70.7%
1y7xA01 2.30.30.550 Mainly Beta › Roll › SH3 type barrels. › Major Vault Protein repeat 0.51 39.0 3.83e-01 100.0% 80.9%
4nohA02 2.40.40.60 Mainly Beta › Beta Barrel › Barwin-like endoglucanases › 0.51 38.0 2.97e-01 83.3% 100.0%
4d10F01 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.51 39.0 2.64e-01 85.7% 89.9%
ECOD (78)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3716713 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.84 75.0 7.08e-01 100.0% 90.0%
3601134 4076.1.1.0 ↗ a+b two layers › L9 N-domain-like › L9 N-domain-like › L9 N-domain-like 0.84 69.0 5.78e-01 100.0% 54.3%
4981952 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.84 75.0 7.08e-01 100.0% 86.0%
4933005 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.83 73.0 6.50e-01 100.0% 75.0%
5000438 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.83 74.0 6.21e-01 100.0% 61.4%
4944185 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.83 75.0 6.39e-01 100.0% 67.7%
4982789 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.83 74.0 6.34e-01 100.0% 67.7%
5036241 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.82 74.0 6.36e-01 100.0% 69.2%
4133267 4076.3.1.3 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › SLD5_C 0.82 71.0 6.58e-01 100.0% 85.5%
4956454 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.82 72.0 6.55e-01 100.0% 74.5%
5069643 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.82 73.0 6.76e-01 100.0% 84.9%
5066664 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.82 71.0 7.01e-01 100.0% 95.6%
4269273 4076.4.1.1 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain › PriS_C 0.81 73.0 7.15e-01 100.0% 97.8%
5044171 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.81 72.0 6.06e-01 100.0% 64.3%
5045837 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.81 71.0 6.35e-01 100.0% 75.0%
3683742 4076.3.1.8 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › PSF2_N 0.81 73.0 6.43e-01 100.0% 70.0%
4935547 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.81 72.0 6.80e-01 100.0% 90.0%
4927873 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.81 72.0 6.37e-01 100.0% 71.7%
4978275 4076.3.1.5 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › Gins51_C 0.81 72.0 6.56e-01 100.0% 83.6%
4932084 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.81 71.0 6.75e-01 100.0% 90.0%
4956746 4076.3.1.5 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › Gins51_C 0.81 72.0 6.78e-01 100.0% 92.0%
4939413 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.81 71.0 6.74e-01 100.0% 96.0%
4973337 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.81 72.0 6.54e-01 100.0% 81.8%
5024995 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.81 71.0 6.62e-01 100.0% 83.0%
5055750 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.81 71.0 6.70e-01 100.0% 90.0%
5019734 4076.3.1.5 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › Gins51_C 0.80 71.0 6.71e-01 100.0% 90.0%
4081421 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.80 70.0 6.68e-01 100.0% 90.0%
5010676 4076.4.1.1 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain › PriS_C 0.80 72.0 6.78e-01 100.0% 86.0%
3818732 4076.3.1.9 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › PSF1_C 0.80 68.0 6.34e-01 100.0% 81.8%
4932061 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.80 72.0 7.05e-01 100.0% 95.6%
4358525 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.80 71.0 6.69e-01 100.0% 86.0%
4994655 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.80 69.0 6.60e-01 100.0% 92.0%
4951589 4076.3.1.5 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › Gins51_C 0.80 70.0 6.67e-01 100.0% 90.0%
4946969 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.80 70.0 6.67e-01 100.0% 92.0%
5011186 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.80 71.0 6.30e-01 100.0% 73.3%
5035786 4076.3.1.5 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › Gins51_C 0.79 69.0 6.55e-01 100.0% 92.0%
4641420 4076.4.1.1 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain › PriS_C 0.79 71.0 5.46e-01 100.0% 47.8%
4613882 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.79 70.0 6.64e-01 100.0% 84.0%
5069341 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.79 70.0 6.63e-01 100.0% 90.0%
5015232 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.79 69.0 6.36e-01 100.0% 80.0%
4304365 4076.3.1.8 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › PSF2_N 0.79 71.0 5.90e-01 100.0% 64.3%
4230268 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.79 70.0 6.85e-01 100.0% 97.8%
1346119 4076.4.1.1 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain › PriS_C 0.79 70.0 6.54e-01 100.0% 84.3%
4956745 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.79 68.0 6.45e-01 100.0% 90.0%
3929869 4076.3.1.8 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › PSF2_N 0.78 70.0 6.39e-01 100.0% 81.8%
4951587 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.78 70.0 6.60e-01 100.0% 84.0%
4967982 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.78 66.0 6.55e-01 97.6% 95.5%
3929096 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.78 66.0 6.30e-01 100.0% 90.0%
5035097 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.78 69.0 6.80e-01 100.0% 93.3%
4460255 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.77 68.0 6.43e-01 100.0% 84.0%
4593896 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.77 69.0 6.74e-01 100.0% 93.3%
5045981 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.77 66.0 6.21e-01 100.0% 88.7%
3940353 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.77 64.0 5.97e-01 100.0% 94.5%
4280403 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.77 66.0 6.52e-01 100.0% 95.6%
5001806 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.76 68.0 6.52e-01 100.0% 87.5%
3168819 4076.3.1.3 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › SLD5_C 0.76 63.0 5.40e-01 100.0% 87.8%
3691283 4076.3.1.9 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › PSF1_C 0.76 64.0 6.16e-01 100.0% 88.0%
4939553 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.76 67.0 6.37e-01 100.0% 84.0%
4169249 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.76 67.0 6.43e-01 100.0% 89.6%
4952672 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.76 63.0 5.92e-01 100.0% 81.8%
3407377 4076.3.1.9 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › PSF1_C 0.76 64.0 5.80e-01 100.0% 76.3%
4934987 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.76 67.0 6.58e-01 100.0% 93.3%
4304386 4076.3.1.3 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › SLD5_C 0.75 62.0 5.99e-01 100.0% 90.0%
4083057 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.75 66.0 6.24e-01 100.0% 84.0%
5036149 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.75 66.0 6.46e-01 100.0% 95.6%
4536596 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.75 65.0 6.24e-01 100.0% 89.6%
5009 4076.3.1.2 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › YqbF 0.75 62.0 5.95e-01 100.0% 83.7%
4419456 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.75 66.0 6.30e-01 100.0% 85.7%
4983060 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.75 65.0 5.28e-01 100.0% 53.8%
4993371 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.74 65.0 6.15e-01 100.0% 86.0%
3600426 4076.3.1.3 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › SLD5_C 0.74 61.0 5.73e-01 100.0% 87.3%
5027046 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.74 63.0 6.02e-01 100.0% 86.0%
4057802 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.74 65.0 6.40e-01 100.0% 93.3%
4988095 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.68 56.0 5.45e-01 100.0% 92.0%
5023430 3529.1.1.0 ↗ beta sandwiches › Major vault protein (MVP) structural repeat domain › Major vault protein (MVP) structural repeat domain › Major vault protein (MVP) structural repeat domain 0.66 51.0 4.79e-01 100.0% 78.3%
5005492 304.122.1.1 ↗ a+b two layers › Alpha-beta plaits › Nitrogen repressor-like proteins › Nitrogen repressor-like proteins › NRD1_2 0.62 50.0 3.87e-01 100.0% 63.6%
4992835 1075.1.2.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain › FtsX 0.56 42.0 2.41e-01 83.3% 27.9%
3601818 10.34.1.0 ↗ beta sandwiches › jelly-roll › Protein CLP1 jelly-roll domain › Protein CLP1 jelly-roll domain 0.54 43.0 3.68e-01 100.0% 81.2%